I painted my whole trans (as always, check my build!), and the block. No problems as long as you don't paint INTO the diptstick hole or over the electronics.
For the inside of the engine, you can try to steam clean it....or just run it and put a few cans of seafoam through it....like...a BUNCH of cans for that much crap.
The black "paddle" bracket thingy is to protect the fuel rail from getting smacked against stuff....I left it one
I have a DIY media blaster locally, so I can just blast it a few days before paint, without too much delay. I've made it one process; media blast, take home, wipe with solvent, dry, paint with primer. After that I can give it however long before color.